Object Light Emission - only on certain surfaces
You can have a object with multiple material. 
In the material panel, there is a small '+' icon on the right, to add a new material slot. And define the second material you want to use. 

Now got to edit mode (Tab), and select the faces you want for this secondary material. Then in the material panel hit assign. 



However, this does not the change that it will be cumbersome for you the select the correct part of your CAD. 

Maybe it's will be easier for you to split your CAD data in various file (or group some pieces in one file) and then in you CAD software export various STL file. Then you'll just have to set a meterial per STL file.